diff --git a/internal/batches/service/service.go b/internal/batches/service/service.go
index 04ad873016..91babe2eef 100644
--- a/internal/batches/service/service.go
+++ b/internal/batches/service/service.go
@@ -648,7 +648,7 @@ func (svc *Service) FindDirectoriesInRepos(ctx context.Context, fileName string,
 		a.WriteString("query DirectoriesContainingFile {\n")
 
 		for _, repo := range batch {
-			query := fmt.Sprintf(`file:(^|/)%s$ repo:^%s$ type:path count:99999`, regexp.QuoteMeta(fileName), regexp.QuoteMeta(repo.Name))
+			query := fmt.Sprintf(`file:(^|/)%s$ repo:^%s$@%s type:path count:99999`, regexp.QuoteMeta(fileName), repo.BaseRef(), regexp.QuoteMeta(repo.Name))
 
 			a.WriteString(fmt.Sprintf(searchQueryTmpl, queryIDByRepo[repo], query))
 		}
diff --git a/internal/batches/service/service_test.go b/internal/batches/service/service_test.go
index 8c6d08d3d6..5539a09815 100644
--- a/internal/batches/service/service_test.go
+++ b/internal/batches/service/service_test.go
@@ -327,8 +327,28 @@ func TestService_FindDirectoriesInRepos(t *testing.T) {
 
 	fileName := "package.json"
 	repos := []*graphql.Repository{
-		{ID: "repo-id-0", Name: "github.com/sourcegraph/automation-testing", Branch: graphql.Branch{Name: "main"}},
-		{ID: "repo-id-1", Name: "github.com/sourcegraph/sourcegraph", Branch: graphql.Branch{Name: "dev"}},
+		{
+			ID:     "repo-id-0",
+			Name:   "github.com/sourcegraph/automation-testing",
+			Branch: graphql.Branch{Name: "dev"},
+			DefaultBranch: &graphql.Branch{
+				Name: "main",
+				Target: graphql.Target{
+					OID: "d34db33f",
+				},
+			},
+		},
+		{
+			ID:     "repo-id-1",
+			Name:   "github.com/sourcegraph/sourcegraph",
+			Branch: graphql.Branch{Name: "dev"},
+			DefaultBranch: &graphql.Branch{
+				Name: "main",
+				Target: graphql.Target{
+					OID: "d34db33f",
+				},
+			},
+		},
 	}
 
 	svc := &Service{client: client}